Does it work if you changes this setting to False?

"Tools->Options->Visual Micro->Compiler Optimization->Library Modified"

What happens if you put breakpoints on real lines of code instead of on comment lines?

What follows is not causing the error but for your information

If you want to share the serial port with the debugger at 9600 speed you should set the LocalSpeed and RemoteSpeed to 9600 in the project property window.

I have tried to change the breakpoints to the other lines and the result is the same. 

The version of .NET Framework is 4.5, I don't know if it should be other version.

I installed it on 21 Sept and the version is this: VisualMicroDebugUpgrade2.msi

I am trying to install again, but it doen'st run, the result is the same. What do you want to say with "run the debug installer from the beta release notes page"?

My version is Arduino 1.0

Email with sketch sent. I don't use the Ardupilot version and I'm going to download the latest Arduino version.

I can't reproduce the debug compile problem you are encountering. Your zip compiles fine for me. I will have to think about what questions I can ask you to find the problem 

Please email me the files from sub directories below your c:\program files\visual micro\Visual Micro for Arduino

Please also confirm which version of visual micro you have installed from Tools>Options>Visual Micro>Version


I have found some other bugs that are not releated to your problem. The debug works at 115200 unless you change the speed in the properties. There seems to be a bug with the system if you attempt to work at a different speed. I have removed your Serial.begin(9600) code, you could add it back in at Serial.begin(115200) if you want. BUT no need until we fix the compile problem 

int cont = 0;

void setup()
{
	pinMode(13,OUTPUT);
}

void loop()
{

  /* add main program code here */
	Serial.println(cont);
	digitalWrite(13, HIGH);
//hhnf
	delay(2000);
	digitalWrite(13, LOW);
	delay(1000);
	cont++;
//vbfgbs

}